[phenixbb] omit maps without density modification?

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Mar 17 14:55:11 PDT 2009

Hi Nathan,

If you generate an omit map with


then all your maps should come from phenix.refine and be the 2FOFCWT
PH2FOFCWT maps which are not density modified.  It may be slightly
confusing because the names of the files will remain the same, and you'll
want to look through the log file to confirm that these are indeed the
maps from phenix.refine.  It will say something like:

Saving 2fofc information in  cycle_best_2.mtz
NOTE: 2fofc map to be used for model-building. It will be copied to
and will also be copied to overall_best_denmod_map_coeffs.mtz

All the best,
Tom T

Is there is a way to calculate simple omit maps and sa-omit maps in phenix
without using density modification?  The density modification seems to be
flattening the weaker regions of my map - when compared to omit maps from
cns for instance.  Thanks!

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